Distinguish between update_dims, extent changes, and refresh (#5363)

* Replace some usage of _update_dims with refresh

* Use extent event instead of set_data

examples/interaction_box_points.py

@@ -36,7 +36,7 @@ def on_transform_changed_drag(event):
 
     for i, index in enumerate(sel_i):
         viewer.layers.selection.active._data[index] = viewer.layers.selection.active.world_to_data(event.value(points[i]))
-    viewer.layers.selection.active._update_dims()
+    viewer.layers.selection.active._clear_extent()
     viewer.layers.selection.active.events.data(value=viewer.layers.selection.active.data)
 
 X, Y = np.mgrid[-500:500:50, -500:500:50]

napari/components/layerlist.py

@@ -94,7 +94,7 @@ def _on_selection_changed(self, event):
 
     def _process_delete_item(self, item: Layer):
         super()._process_delete_item(item)
-        item.events.set_data.disconnect(self._clean_cache)
+        item.events.extent.disconnect(self._clean_cache)
         self._clean_cache()
 
     def _clean_cache(self):
@@ -163,7 +163,7 @@ def insert(self, index: int, value: Layer):
         new_layer = self._type_check(value)
         new_layer.name = self._coerce_name(new_layer.name)
         self._clean_cache()
-        new_layer.events.set_data.connect(self._clean_cache)
+        new_layer.events.extent.connect(self._clean_cache)
         super().insert(index, new_layer)
 
     def toggle_selected_visibility(self):

napari/layers/base/base.py

@@ -343,6 +343,7 @@ def __init__(
             cursor_size=Event,
             editable=Event,
             loaded=Event,
+            extent=Event,
             _ndisplay=Event,
             select=WarningEmitter(
                 trans._(
@@ -551,7 +552,7 @@ def scale(self, scale):
         if scale is None:
             scale = [1] * self.ndim
         self._transforms['data2physical'].scale = np.array(scale)
-        self._update_dims()
+        self._clear_extent()
         self.events.scale()
 
     @property
@@ -562,7 +563,7 @@ def translate(self):
     @translate.setter
     def translate(self, translate):
         self._transforms['data2physical'].translate = np.array(translate)
-        self._update_dims()
+        self._clear_extent()
         self.events.translate()
 
     @property
@@ -573,7 +574,7 @@ def rotate(self):
     @rotate.setter
     def rotate(self, rotate):
         self._transforms['data2physical'].rotate = rotate
-        self._update_dims()
+        self._clear_extent()
         self.events.rotate()
 
     @property
@@ -584,7 +585,7 @@ def shear(self):
     @shear.setter
     def shear(self, shear):
         self._transforms['data2physical'].shear = shear
-        self._update_dims()
+        self._clear_extent()
         self.events.shear()
 
     @property
@@ -600,7 +601,7 @@ def affine(self, affine):
         self._transforms[2] = coerce_affine(
             affine, ndim=self.ndim, name='physical2world'
         )
-        self._update_dims()
+        self._clear_extent()
         self.events.affine()
 
     @property
@@ -648,12 +649,8 @@ def _is_moving(self, value):
             assert self._moving_coordinates is not None
         self._private_is_moving = value
 
-    def _update_dims(self, event=None):
-        """Update the dims model and clear the extent cache.
-
-        This function needs to be called whenever data or transform information
-        changes, and should be called before events get emitted.
-        """
+    def _update_dims(self):
+        """Update the dimensionality of transforms and slices when data changes."""
         ndim = self._get_ndim()
 
         old_ndim = self._ndim
@@ -667,10 +664,8 @@ def _update_dims(self, event=None):
         self._slice_input = self._slice_input.with_ndim(ndim)
 
         self._ndim = ndim
-        if 'extent' in self.__dict__:
-            del self.extent
 
-        self.refresh()  # This call is need for invalidate cache of extent in LayerList. If you remove it pleas ad another workaround.
+        self._clear_extent()
 
     @property
     @abstractmethod
@@ -721,6 +716,18 @@ def extent(self) -> Extent:
             step=abs(data_to_world.scale),
         )
 
+    def _clear_extent(self):
+        """Clears the cached extent.
+
+        This should be called whenever this data or transform information
+        changes, and should be called before any related events get emitted
+        so that they use the updated extent values.
+        """
+        if 'extent' in self.__dict__:
+            del self.extent
+        self.events.extent()
+        self.refresh()
+
     @property
     def _slice_indices(self):
         """(D, ) array: Slice indices in data coordinates."""
@@ -919,8 +926,7 @@ def _slice_dims(self, point=None, ndisplay=2, order=None):
         if old_ndisplay != ndisplay:
             self.events._ndisplay()
 
-        # Update the point values
-        self._update_dims()
+        self.refresh()
         self._set_editable()
 
     def _make_slice_input(
@@ -1136,7 +1142,7 @@ def refresh(self, event=None):
         """Refresh all layer data based on current view slice."""
         if self.visible:
             self.set_view_slice()
-            self.events.set_data()  # refresh is called in _update_dims which means that extent cache is invalidated. Then, base on this event extent cache in layerlist is invalidated.
+            self.events.set_data()
             self._update_thumbnail()
             self._set_highlight(force=True)
 

napari/layers/image/image.py

@@ -372,7 +372,7 @@ def __init__(
         # where the intention here is to use the base setter, so we use the
         # _set_colormap method. This is important for Labels layers, because
         # we don't want to use get_color before set_view_slice has been
-        # triggered (self._update_dims(), below).
+        # triggered (self.refresh(), below).
         self._set_colormap(colormap)
         self.contrast_limits = self._contrast_limits
         self._interpolation2d = Interpolation.NEAREST
@@ -386,7 +386,7 @@ def __init__(
         connect_no_arg(self.plane.events, self.events, 'plane')
 
         # Trigger generation of view slice and thumbnail
-        self._update_dims()
+        self.refresh()
 
     def _new_empty_slice(self):
         """Initialize the current slice to an empty image."""

napari/layers/labels/labels.py

@@ -307,7 +307,7 @@ def __init__(
         self._reset_history()
 
         # Trigger generation of view slice and thumbnail
-        self._update_dims()
+        self.refresh()
         self._set_editable()
 
     @property

napari/layers/points/points.py

@@ -467,7 +467,7 @@ def __init__(
         self.antialiasing = antialiasing
 
         # Trigger generation of view slice and thumbnail
-        self._update_dims()
+        self.refresh()
 
     @property
     def data(self) -> np.ndarray:

napari/layers/shapes/shapes.py

@@ -558,7 +558,7 @@ def __init__(
         )
 
         # Trigger generation of view slice and thumbnail
-        self._update_dims()
+        self.refresh()
 
     def _initialize_current_color_for_empty_layer(
         self, color: ColorType, attribute: str

napari/layers/surface/surface.py

@@ -203,7 +203,7 @@ def __init__(
         if len(data) not in (2, 3):
             raise ValueError(
                 trans._(
-                    'Surface data tuple must be 2 or 3, specifying verictes, faces, and optionally vertex values, instead got length {length}.',
+                    'Surface data tuple must be 2 or 3, specifying vertices, faces, and optionally vertex values, instead got length {length}.',
                     deferred=True,
                     length=len(data),
                 )
@@ -230,7 +230,9 @@ def __init__(
         self._view_faces = np.zeros((0, 3))
         self._view_vertex_values = []
 
-        # Trigger generation of view slice and thumbnail
+        # Trigger generation of view slice and thumbnail.
+        # Use _update_dims instead of refresh here because _get_ndim is
+        # dependent on vertex_values as well as vertices.
         self._update_dims()
 
         # Shading mode
@@ -283,7 +285,6 @@ def vertices(self, vertices):
         self._vertices = vertices
 
         self._update_dims()
-        self.refresh()
         self.events.data(value=self.data)
         self._set_editable()
 
@@ -297,7 +298,7 @@ def vertex_values(self, vertex_values: np.ndarray):
 
         self._vertex_values = vertex_values
 
-        self.refresh()
+        self._update_dims()
         self.events.data(value=self.data)
         self._set_editable()
 

napari/layers/tracks/tracks.py

@@ -195,7 +195,7 @@ def __init__(
         self.color_by = color_by
         self.colormap = colormap
 
-        self._update_dims()
+        self.refresh()
 
         # reset the display before returning
         self._current_displayed_dims = None

napari/layers/utils/_link_layers.py

@@ -188,7 +188,7 @@ def layers_linked(layers: Iterable[Layer], attributes: Iterable[str] = ()):
 
 def _get_common_evented_attributes(
     layers: Iterable[Layer],
-    exclude: set[str] = {'thumbnail', 'status', 'name', 'data'},
+    exclude: set[str] = {'thumbnail', 'status', 'name', 'data', 'extent'},
     with_private=False,
 ) -> set[str]:
     """Get the set of common, non-private evented attributes in ``layers``.

napari/layers/vectors/vectors.py

@@ -245,7 +245,7 @@ def __init__(
         self._view_alphas = []
 
         # now that everything is set up, make the layer visible (if set to visible)
-        self._update_dims()
+        self.refresh()
         self.visible = visible
 
     @property